Quantitative trait locus analysis in crosses between outbred lines with dominance and inbreeding

We provide a theoretical framework for quantitative trait locus (QTL) analy sis of a crossed population where parental lines may be outbred and dominan ce as well as inbreeding are allowed for. It can be applied to any pedigree . A biallelic QTL is assumed, and the QTL allele frequencies can be differe nt in each breed. The genetic covariance between any two individuals is exp ressed as a nonlinear function of the probability of up to 15 possible iden tity modes and of the additive and dominance effects, together with the all elic frequencies in each of the two parental breeds. The probabilities of e ach identity mode are obtained at the desired genome positions using a Mont e Carlo Markov chain method. Unbiased estimates of the actual genetic param eters are recovered in a simulated F-2 cross and in a six-generation comple x pedigree under a variety, of genetic models (allele fixed or segregating in the parental populations and additive or dominance action). Results from analyzing an F-2 cross between Meishan and Large White pigs are also prese nted.